Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate 8501405 DvMF_2135 TRAP dicarboxylate transporter, DctP subunit (RefSeq)
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__Miya:8501405 Length = 365 Score = 143 bits (360), Expect = 8e-39 Identities = 93/290 (32%), Positives = 152/290 (52%), Gaps = 7/290 (2%) Query: 5 RILGALVGATALSLALSVPA----LAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNG 60 R L A +G LA +P + + + V P + + A +F +L E+ ++G Sbjct: 31 RALAASLGLMLACLAAILPGWPRTASAATELTLAVVTTPGSAQHVCAERFRQLLEERSHG 90 Query: 61 AVDVEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEAL 120 A V V+ + L + E L+ LQLG VQ+ +L P V + +V D P++F+D Sbjct: 91 AYRVVVHHSGTLGTETEILQQLQLGGVQLAIITLGVLDPF-VPEVKVLDYPFLFRDAAEA 149 Query: 121 HKVTQGEAGKMLLSKLEAKGITGLAFWDNGFKIMSANT-PLTMPDDFLGLKMRIQSSKVL 179 +V G G+ LL LE G+ GL F +NGF+ ++ N P+ DD GLK+R+ S + Sbjct: 150 DRVLDGATGRALLDALERVGLKGLHFSENGFRHLTNNVRPVRSVDDVRGLKIRVLESTLH 209 Query: 180 EAEMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGY 239 ALGA P M + +Y LQ G +DG ENP M +M EVQK+ +++ H Y + Sbjct: 210 RELWRALGANPTPMGWP-IYAELQQGTIDGQENPLWVMAEYRMPEVQKYLSLTGHVYSAH 268 Query: 240 AVIVNKQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAG 289 A + N +++GLP RT + + MA++ Y ++++ L+ +++AG Sbjct: 269 ADLANLAWFNGLPPAERTLVMQCMADAAAYQRAYNRQKDADYLRRLREAG 318 Lambda K H 0.314 0.130 0.364 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 211 Number of extensions: 7 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 333 Length of database: 365 Length adjustment: 29 Effective length of query: 304 Effective length of database: 336 Effective search space: 102144 Effective search space used: 102144 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory